Nima Hejazi

Login: nhejazi

Company: UC Berkeley

Location: Oakland, CA, USA

Bio: biostatistics phd student ? causal inference ? nonparametrics and machine learning ? statistical and scientific computing

Blog: https://nimahejazi.org

Blog: https://nimahejazi.org

Member of

2. Reproducible Science Curriculum
3. Software Carpentry
4. The Hacker Within
5. The Hubbard Group
6. The van der Laan Group
7. tlverse

Repositories

2018-05-03-LBNL

Data Carpentry workshop, Lawrence Berkeley National Laboratory, 3-4 May

23-and-i

:bar_chart: workflow to play with genomic data from 23andMe SNPs (for my genome)

538data

Data and code behind the stories and interactives at FiveThirtyEight

adaptest

:package: :microscope: R/adaptest: Data-Adaptive Procedures for Multiple Hypothesis Testing in High-Dimensional Biology

almost_surely_blog

:pencil: "Almost Surely" - just another blog on statistics, machine learning, and data science

astro250-python-computing

:school_satchel: Python for Data Science (Astronomy 250 seminar course at UC Berkeley)

awesome-machine-learning

A curated list of awesome Machine Learning frameworks, libraries and software.

awesome-public-datasets

An awesome list of high-quality open datasets in public domains (on-going).

awesome-python

A curated list of awesome Python frameworks, libraries, software and resources

berkeleyTHW

The Hacker Within at the University of California - Berkeley

biomedical-datasci

:book: Rmd source files for the HarvardX series PH525x

biotmle

:package: :microscope: R/biotmle: Targeted Learning with Variance Stabilization for Biomarker Discovery

biotmleData

:package: Bioconductor data package associated with the biotmle R package

coloremoji.sty

Style package for directly including color emojis in latex documents

condensier

Semi-parametric conditional density estimation

conf_ACIC-txshift-2018

Poster "Robust Nonparametric Inference for Stochastic Interventions Under Multi-Stage Sampling" for the Atlantic Causal Inference Conference, May 2018

conf_CRM-poster-comp-2016

:bar_chart: Entry using Super Learner for the causal inference challenge at CRM 2016

ctmle

Collaborative Targeted Maximum Likelihood Estimation

cvma

Cross-validation-based maximal associations

datamicroarray

A collection of small-sample, high-dimensional microarray data sets to assess machine-learning algorithms and models.

DataScience-coursera-materials

Course materials for the JHSPH-Coursera Data Science Specialization

data-science-ipython-notebooks

Continually updated data science Python notebooks: Deep learning (TensorFlow, Theano, Caffe), scikit-learn, Kaggle, big data (Spark, Hadoop MapReduce, HDFS), matplotlib, pandas, NumPy, SciPy, Python essentials, AWS, and various command lines.

deepdream

null

deeplearning-papernotes

Summaries and notes on Deep Learning research papers

deep-learning-with-r-notebooks

Jupyter notebooks for the code samples of the book "Deep Learning with Python"

deeplrn-dsm2lec

Slides and Jupyter notebooks for the Deep Learning lectures at M2 Data Science Université Paris Saclay

deeplrn-fastai-materials

fast.ai Courses

deepo

A Docker image containing almost all popular deep learning frameworks: theano, tensorflow, sonnet, pytorch, keras, lasagne, mxnet, cntk, chainer, caffe, torch.

delayed

:package: :wrench: Dependent delayed computation for R

drtmle

Nonparametric estimators of the average treatment effect with doubly-robust confidence intervals and hypothesis tests

fastai

The fast.ai deep learning library, lessons, and tutorials

fitbit

:chart_with_upwards_trend: workflow to play with data collected by Fitbit (written for my personal activity data)

free-programming-books

:books: Freely available programming books

ggplot2

An implementation of the Grammar of Graphics in R

git-flight-rules

Flight rules for git

git-novice

Software Carpentry introduction to Git for novices.

good-news

A bit of entertainment for when your head is stuck in a :shell:...

grf

Generalized Random Forests

hal9001

:package: :crystal_ball: R/hal9001: The nonparametric Highly Adaptive LASSO estimator meets speed and scalability

hugo-academic

The personal website framework for Hugo. Demo at

hugo-blackburn

A Hugo theme built using Yahoo's Pure CSS

hugo-bootstrap-premium

Hugo appernetic bootstrap premium theme

hugo-future-imperfect

A ported theme with some extras for the Hugo static website engine

hugo-goa

Simple Minimalistic Theme for Hugo

hugo-kiss

Stupidly simple Hugo blogging theme

hugo-minimal

Personal blog theme powered by Hugo

introduction_to_ml_with_python

Notebooks and code for the book "Introduction to Machine Learning with Python"

junkdrawer

:open_file_folder: assorted collection of short scripts and how-tos

labnotebook

:notebook: notes from research group/lab meetings

lobstr

Understanding complex R objects with tools similar to str()

Machine-Learning-Tutorials

machine learning and deep learning tutorials, articles and other resources

macOS-fresh

:computer: customization scripts for fresh installs of macOS

MathsDL-spring18

Topics course Mathematics of Deep Learning, NYU, Spring 18

medical-ML-data

null

methyvim

:package: :microscope: R/methyvim: Targeted Learning of Variable Importance Measures for Differential Methylation Analysis

methyvimData

:package: Bioconductor data package associated with the methyvim R package

mlens

ML-Ensemble ? high performance ensemble learning

ML_for_Hackers

Code accompanying the book "Machine Learning for Hackers"

mlpack

mlpack: a scalable C++ machine learning library --

mlr

mlr: Machine Learning in R

mydots

:wrench: :computer: personalized config file collection for Linux and macOS machines

myhammerspoon

:computer: custom config for the macOS management tool Hammerspoon

myPkgLib

:computer: convenience scripts for easily setting up package libraries

neuralnets-sandbox

Notes and work for learning about neural networks and deep learning, primarily focused around experimenting with modern frameworks

neurodevstat

:mag: Curated statistical (re)analysis of publicly available RNA-Seq transcriptome data from a study on human brain development

nhejazi.github.io

:earth_americas: personal website (this is just a redirect https://nhejazi.github.io :point_right: https://code.nimahejazi.org)

nima

:package: :wrench: R/nima: The personal R toolbox of Nima Hejazi

notes-hpcSavio

:notebook: collection of resources on using Berkeley's HPC Savio cluster

npcausal

null

numerical-linear-algebra

This course contains the notebooks for the Numerical Linear Algebra elective in USF's MSAN program, summer 2017

opttx2

:package: :pill: R/opttx2: Estimation of Optimal Treatment Effects

origami

:package: :wrench: R/origami: High-powered and Generalizable Framework for Cross-Validation

papers-we-love

Papers from the computer science community to read and discuss.

parsnip

A tidy unified interface to models

pattern_classification

A collection of tutorials and examples for solving and understanding machine learning and pattern classification tasks

ph240d-benzene-biomarkers

:school_satchel: course project for Computational Statistics with Applications in Biology and Medicine, UC Berkeley

ph240f-scRNAseq-joost

:school_satchel: UC Berkeley's Public Health C240F (Statistical Genomics), Spring 2017: (re)analysis of public scRNA-seq data

ph242c-longit-data

:school_satchel: presentation materials for course project for Longitudinal Data Analysis, UC Berkeley

ph295-targeted-limma

:school_satchel: UC Berkeley's Public Health 295 (Targeted Learning with Biomedical Big Data), Fall 2016, Final Project: the moderated t-statistic with asymptotically linear parameters

ph295-tlbbd-fall2016

:school_satchel: Lab materials for Targeted Learning with Biomedical Big Data (PH 295 seminar, Fall 2016, UC Berkeley)

pkgdown_rmd

Example R package for pkgdown issue #394

ProjectTemplate

A template utility for R projects that provides a skeletal project.

pydata-book

Materials and IPython notebooks for "Python for Data Analysis" by Wes McKinney, published by O'Reilly Media

python-bootcamp

:school_satchel: docs and lectures for the Python Bootcamp at UC Berkeley

PythonDataScienceHandbook

Jupyter Notebooks for the Python Data Science Handbook

python-guide

Python best practices guidebook, written for Humans.

python-machine-learning-book

The "Python Machine Learning" book code repository and info resource

pytorch

Tensors and Dynamic neural networks in Python with strong GPU acceleration

pytorch-examples

A set of examples around pytorch in Vision, Text, Reinforcement Learning, etc.

pytudes

Python programs to practice or demonstrate skills.

quotable

:thought_balloon: a growing collection of awesome and inspiring quotes...

r-bootcamp-2016

:school_satchel: 2016 iteration of the R Bootcamp at UC Berkeley

r-bootcamp-2017

R bootcamp at UC Berkeley, sponsored by the Department of Statistics and the D-Lab, August 2017

repro-case-studies

Reproducibility case study contributions

reveal.js

The HTML Presentation Framework

r-novice-gapminder

Introduction to R for non-programmers using gapminder data.

rpkgs-meta

:notebook: :computer: Collection of R packages that I have developed or played a primary role in co-developing

rsample

Classes and functions to create and summarize different types of resampling objects

scikit-learn

scikit-learn: machine learning in Python

shablona

A template for small scientific python projects

sisbid-repro_res-2017

Materials for Module 3 of the SISBID Workshop, Reproducible Research

skorch

A scikit-learn compatible neural network library that wraps pytorch

sl3

:package: :crystal_ball: R/sl3: A modern toolkit for the Super Learner algorithm and generalized machine learning pipelines

sl3_lecture

:notebook: ?? An introductory workshop lecture on ensemble machine learning with pipelines using the sl3 R package

sl3_lecture

:notebook: ?? An introductory workshop lecture on ensemble machine learning with pipelines using the sl3 R package

sonnet

TensorFlow-based neural network library

stat159-repro-datasci

:school_satchel: course project for Reproducible and Collaborative Statistical Data Science, UC Berkeley

stat212b-deep-learning

:school_satchel: special topics course on Deep Learning, Dept. of Statistics, UC Berkeley

stat215a-journal-review

:bar_chart: UC Berkeley's Statistics 215A (Applied Statistics), Fall 2016: Journal Refereeing Project

stat337-datasci-readings

Readings in applied data science

stat-learning

Notes and exercise attempts for "An Introduction to Statistical Learning"

statsrefs

:closed_book: BibTeX collection of common references for my Statistics manuscripts

strava

Create artistic visualisations with your exercise data

survtmle

:package: :hourglass_flowing_sand: R/survtmle: Targeted Learning for Survival Analysis

talk_admitday-stats

:speech_balloon: Talk on research in (bio)statistics for newly admitted undergraduate and graduate students at UC Berkeley

talk_admitday-stats

:speech_balloon: Talk on research in (bio)statistics for newly admitted undergraduate and graduate students at UC Berkeley

talk_admitday-stats

:speech_balloon: Talk on research in (bio)statistics for newly admitted undergraduate and graduate students at UC Berkeley

talk_admitday-stats

:speech_balloon: Talk on research in (bio)statistics for newly admitted undergraduate and graduate students at UC Berkeley

talk_biotmle

:speech_balloon: Talk on applying empirical Bayes statistics to asymptotically linear parameters

talk_fair-outcomes

:speech_balloon: Talk on "Fair Inference on Outcomes" (R. Nabi & I. Shpitser, 2017), for M. Hardt's "Fairness in Machine Learning" seminar at Berkeley, Fall 2017

talk_futuRe-intro

:speech_balloon: Minimal tutorial on flexible parallel computing with futures in R

talk_h2oSL-THW

:speech_balloon: Presentation on "Ensemble (Machine) Learning with Super Learner and H2O in R" for The Hacker Within on 6 December 2016

talk_itb

:speech_balloon: Talk: "Evaluating Survival Prognosis in the Presence of Immortal Time Bias"

talk_lstm-seq2seq

:speech_balloon: Talk on "Sequence to Sequence Learning with Neural Networks" (I. Sutskever et al., 2014), for the seminar "Deep Time-Series Learning with Finance Applications" at Berkeley, Fall 2017

talk_methyvim

:speech_balloon: Talk: "Data-Adaptive Estimation and Inference in the Analysis of Differential Methylation"

talk_scrna-diffexp

:speech_balloon: Talk comparing two recent methods for differential expression analysis with single-cell RNA-seq data

talk_sensitivity-ipw

:speech_balloon: Talk on "Sensitivity Analysis for Inverse Probability Weighting Estimators via the Percentile Bootstrap" (Q. Zhao et al., 2017), for S. Pimentel's "Observational Study Design and Causal Inference" seminar at Berkeley, Spring 2018

talk_txshift

:speech_balloon: Talk: "Robust Nonparametric Inference for Stochastic Interventions Under Multi-Stage Sampling"

template_posters

Template for LaTeX conference posters

template_talks-md

:page_facing_up: Template for beamer slide decks using Markdown and Pandoc

template_talks-tex

:page_facing_up: Template for slide decks using LaTeX beamer

thesisdown

An updated R Markdown thesis template using the bookdown package

thesis-masters-biostat

:black_nib: Biostatistics M.A. thesis: "Generalized application of empirical Bayes statistics to asymptotically linear parameters"

tlbbd

Teaching materials for TLBBD

tlverse.org

null

tmle3

:package: :wrench: R/tmle3: Framework for Computing Targeted Maximum Likelihood Estimators for Causal/Statistical Inference

tmle3_lecture

null

tmle3shift

null

tstmle

Estimation and Inference for Context-Specific Causal Average Treatment Effect and Optimal Individualized Treatment Effect with Single Time Series

tutorials_stock_prediction

null

txshift

:package: :syringe: R/txshift: Causal inference and variable importance for the effects of stochastic interventions with Targeted Learning

ubuntu-fresh

:computer: customization scripts for fresh installs of Ubuntu

useR-machine-learning-tutorial

useR! 2016 Tutorial: Machine Learning Algorithmic Deep Dive http://user2016.org/tutorials/10.html

vimForLife

:black_nib: once-minimalist but now convenient configurations for the Vim and Neovim editors

vimp

Nonparametric variable importance assessment

workarchive

:open_file_folder: An archive of my presentations, posters, and publications for mirroring on departmental websites

Commits To